depristo
|
669d9096e3
|
now support -o output option, useful for pipelines
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3959 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-06 14:57:04 +00:00 |
chartl
|
6dcb63888d
|
Be smart about the headers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3912 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-30 16:11:16 +00:00 |
|
chartl
|
eeb767a012
|
Remove legacy "out"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3911 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-30 15:01:02 +00:00 |
|
chartl
|
f20cdbe60a
|
Modified to work with MT containing VCFs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3910 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-30 14:59:59 +00:00 |
|
chartl
|
52f24c86fa
|
Script to split a provided interval list into contigs. Excesses will be dropped into the last provided file. Works like splitIntervals.sh. This is for Queue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3895 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-29 16:42:53 +00:00 |
corin
|
3596b1529f
|
module for listing out samples for data processing and firehose reporting
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3847 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-21 15:05:41 +00:00 |
|
corin
|
1209b165bf
|
Now accepts command line args and prints paths to vcf, bams and beds
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3846 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-07-21 15:04:58 +00:00 |
|
depristo
|
2bdb011865
|
Improvements to 1KG processing pipeline
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3807 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-16 15:33:47 +00:00 |
|
corin
|
74f705d943
|
fixed silly syntax errors
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3805 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-16 15:08:46 +00:00 |
|
corin
|
917469ef43
|
This script produces information for a firehose job-finished email
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3804 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-16 14:44:52 +00:00 |
|
chartl
|
19a5830186
|
Restore "type" annotation (but not genomechange or cDNA change, which are already encoded in the VCF)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3784 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-13 17:33:15 +00:00 |
|
chartl
|
9cc1a411b2
|
Altering the formatting of the annotation to work better with VariantEval's AminoAcidTransition
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3782 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-13 16:31:14 +00:00 |
|
chartl
|
80a5ddfa2f
|
Memory string added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3771 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-07-12 20:43:19 +00:00 |
|
chartl
|
46c39f2d53
|
Quick python scripts for going from genotype VCFs to site-only VCFs, and one to fix BC vcf files (which had "het" genotypes at non-variant sites)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3768 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-12 19:13:32 +00:00 |
|
depristo
|
dd978dd525
|
misc. changes to python scripts
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3751 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-07-09 00:13:35 +00:00 |
|
depristo
|
cf910d9cc2
|
misc. useful updates to python library
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3683 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-06-30 16:33:32 +00:00 |
weisburd
|
e7939f7036
|
Fixed error message
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3653 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-06-28 14:50:28 +00:00 |
|
weisburd
|
1cb8f51f8c
|
Fixed -t arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3634 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-06-24 23:44:10 +00:00 |
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weisburd
|
3cd0570c1e
|
Now can run with multiple processes, multiple threads, or both
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3633 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 23:25:01 +00:00 |
|
weisburd
|
dae3ce2c0f
|
changed log dir
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3632 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 23:08:13 +00:00 |
|
weisburd
|
fea8054e9e
|
Updated long name for -l to --run-locally
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3631 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 22:26:45 +00:00 |
|
weisburd
|
72e669538e
|
Updated arg description for -s
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3629 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 22:04:01 +00:00 |
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weisburd
|
cef12b45e1
|
Fixed typo
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3561 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-15 21:17:14 +00:00 |
|
weisburd
|
c0370f4d0a
|
Added both inclusive and exclusive filters
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3538 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-11 18:40:41 +00:00 |
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weisburd
|
d1a4c4f0d3
|
Added -w filter option allowing user to specify chromosomes to be skipped.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3531 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-06-10 20:58:25 +00:00 |
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weisburd
|
6fd2d39a7d
|
Modified run_locally mode to use os.system(..) instead of popen
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3515 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-09 17:10:03 +00:00 |
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weisburd
|
a3ccf49f5b
|
Write error to stderr
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3514 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-09 17:09:10 +00:00 |
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weisburd
|
2b31975cb4
|
Added more options for coordinate systems - now you can add 1 to either the start coordinates, the end coordinates, or both
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3508 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-06-08 22:49:19 +00:00 |
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weisburd
|
410afcdf2c
|
Added parallelization options - when running locally, multiple processes can be spawned, or a -nt arg can be specified to run each TranscriptToInfo instance multi-threaded
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3507 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:48:07 +00:00 |
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weisburd
|
92c72d3361
|
Added back lines that update the *big-table-header.txt file before using it
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3506 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:45:41 +00:00 |
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weisburd
|
3c24223d02
|
Script for concatenating 2 AnnotatorInputTables, and writing the result to standard out. Merge-sorts the 2 tables while concatenating them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3505 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:44:16 +00:00 |
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depristo
|
f32a32269c
|
minor change for eric
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3418 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-21 20:13:36 +00:00 |
|
depristo
|
d1098fa77b
|
Removing unnecessary dependences that were causing problems for Sendu
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3410 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-21 13:07:41 +00:00 |
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depristo
|
886e9c1297
|
Now can take a VCF file as input
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3378 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-05-18 17:06:12 +00:00 |
|
depristo
|
2a212c497f
|
minor improvements and bug fixes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3376 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-05-18 15:54:42 +00:00 |
|
depristo
|
43544cfdf9
|
remote control of IGV to jump to any number of loci in a file and screenshot the locus to a file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3375 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-05-18 12:59:36 +00:00 |
|
weisburd
|
04e14ef85a
|
Refactored so it could be used for knownGene and CCDS as well as refGene
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3373 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-05-18 02:45:11 +00:00 |
|
depristo
|
2a803e9044
|
simple tool that takes two dbSNP files and subsets the seconds to only include rsID SNPs present in the first. Used to make b129 against b37 by subsetting b131/b37 vs. b129/b36
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3352 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-05-12 13:39:09 +00:00 |
|
depristo
|
d3c33d4b3f
|
more powerful management routines for my pipeline
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3351 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-12 13:37:39 +00:00 |
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weisburd
|
f120a00433
|
Fixed bug so that the strand, alternate, and reference columns are now moved correctly
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3342 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-05-10 17:59:39 +00:00 |
|
depristo
|
d6b036cdab
|
Minor improvements to simple python code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3330 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-07 21:34:46 +00:00 |
|
chartl
|
d5b675b3e6
|
Added - Q&D script to gather verbose bed files to a VCF.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3294 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-05 02:49:16 +00:00 |
|
weisburd
|
a462b5e1e7
|
Changed a default path
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3291 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-05-03 17:07:21 +00:00 |
|
weisburd
|
28f746b76a
|
Added option to generate UCSC or NCBI sequence
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3283 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-04-30 17:26:00 +00:00 |
|
weisburd
|
c214056d88
|
Script for concatenating results of GenerateTranscriptToInfo.py into one big file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3279 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-04-30 15:47:08 +00:00 |
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weisburd
|
0069cb426d
|
Script for spawning LSF jobs that run the TranscriptToInfo.java walker on each of the 50 contigs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3277 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-04-30 15:27:52 +00:00 |
|
weisburd
|
ba7fe7c4e1
|
Renamed
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3276 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:25:07 +00:00 |
|
weisburd
|
4937295a0b
|
Renamed
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3275 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:24:56 +00:00 |
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depristo
|
bf3dbd8401
|
some useful routines for working with project processing. madPipeline contains a bunch of useful routines for building pipelines that I finally put into one file. Let's just say that I'm really looking forward to the new pipeline system...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3260 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-04-26 12:34:04 +00:00 |
|
weisburd
|
c7b4f78316
|
Added -m arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3233 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-04-21 22:38:47 +00:00 |